Hi Kathryn, mauveAligner appears to have an "undocumented feature" whereby it also requires --mums --no-recursion to be part of the repeat generation command-line. The requirement is a bit silly, and it will probably change in a future release. Anyways, I tested repeat generation on a raw shotgun read dataset (Bacteriodes fragilis) and it ran quickly.
The working command-line was: mauveAligner --repeats --output=fragilis.repeats --no-recursion --mums BF638R_shotgun.fas BF638R_shotgun.fas.sml I've logged the "undocumented feature" as a bug in our sourceforge tracker: http://sourceforge.net/tracker/index.php?func=detail&aid=1839271&group_id=181544&atid=897627 Regards, -Aaron Kathryn Holt wrote: > I'm trying to use the --repeats option with mauveAligner. > I keep getting the message: > "A paramater has been specified that is incompatible with repeat list > generation" > even when --repeats is the only option specified before my sequence file. > What am I doing wrong? This is the Linux 2.1 version. > Thanks, > Kathryn > > > ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
